2014
Comparative analysis of pseudogenes across three phyla
Sisu C, Pei B, Leng J, Frankish A, Zhang Y, Balasubramanian S, Harte R, Wang D, Rutenberg-Schoenberg M, Clark W, Diekhans M, Rozowsky J, Hubbard T, Harrow J, Gerstein MB. Comparative analysis of pseudogenes across three phyla. Proceedings Of The National Academy Of Sciences Of The United States Of America 2014, 111: 13361-13366. PMID: 25157146, PMCID: PMC4169933, DOI: 10.1073/pnas.1407293111.Peer-Reviewed Original ResearchConceptsGenome evolutionLarge effective population sizesNumerous duplication eventsProtein-coding genesNumber of pseudogenesEffective population sizePotential regulatory roleDuplication eventsSelective sweepsGene familyHuman pseudogenesPrimate lineageDifferent remodeling processesPseudogenesUpstream sequencesHigh deletion ratePromoter activityBiochemical activityRegulatory rolePopulation sizePartial activityGenomePhylaDeletion rateLineages
2011
tcf21+ epicardial cells adopt non-myocardial fates during zebrafish heart development and regeneration
Kikuchi K, Gupta V, Wang J, Holdway JE, Wills AA, Fang Y, Poss KD. tcf21+ epicardial cells adopt non-myocardial fates during zebrafish heart development and regeneration. Development 2011, 138: 2895-2902. PMID: 21653610, PMCID: PMC3119303, DOI: 10.1242/dev.067041.Peer-Reviewed Original ResearchConceptsHeart developmentZebrafish heart developmentRecent lineage-tracing studiesLineage-tracing studiesEmbryonic developmentUpstream sequencesHeart regenerationCell typesEpicardial cellsDevelopmental potentialCardiac muscle cellsZebrafishTCF21Muscle cellsPerivascular cellsCellsFateRegenerationCardiogenesisLarvalEpicardial tissueSequenceExpressionDevelopment
2007
Molecular Actions of 1,25‐Dihydroxyvitamin D3 on Genes Involved in Calcium Homeostasis*
Pike JW, Zella LA, Meyer MB, Fretz JA, Kim S. Molecular Actions of 1,25‐Dihydroxyvitamin D3 on Genes Involved in Calcium Homeostasis*. Journal Of Bone And Mineral Research 2007, 22: v16-v19. PMID: 18290714, DOI: 10.1359/jbmr.07s207.Peer-Reviewed Original ResearchConceptsTranscriptional start siteRegulatory regionsExpression of TRPV6RANKL geneKey regulatory regionsVertebrate organismsNovel genesChromatin immunoprecipitationStart siteRegulatory elementsUpstream sequencesGene expressionEnhancer regionMolecular mechanismsHuman TRPV6Upstream regionGenesTRPV6 geneMolecular actionsMolecular techniquesPrimary regulatorMicroarray methodKbTRPV6Expression
2006
GATA‐3 regulates the transcriptional activity of tyrosine hydroxylase by interacting with CREB
Hong S, Huh Y, Chae H, Hong S, Lardaro T, Kim K. GATA‐3 regulates the transcriptional activity of tyrosine hydroxylase by interacting with CREB. Journal Of Neurochemistry 2006, 98: 773-781. PMID: 16893419, DOI: 10.1111/j.1471-4159.2006.03924.x.Peer-Reviewed Original ResearchConceptsCAMP response elementGATA-3 binding sitesProtein-protein interaction assaysTH promoterProtein-protein interactionsSite-directed mutationsNeural crest stem cellsGATA-3TH gene transcriptionUpstream sequencesInteraction assaysTyrosine hydroxylaseAbolished transactivationBinding motifTranscription factor GATA-3Transcriptional activityTranscription factorsEmbryonic lethalityPromoter functionResponse elementGene transcriptionTarget gene(sTranscriptional activation of tyrosine hydroxylaseCell developmentExpression of GATA-3
2003
Characterization of the Human Lung CYP2F1 Gene and Identification of a Novel Lung-specific Binding Motif*
Carr B, Wan J, Hines R, Yost G. Characterization of the Human Lung CYP2F1 Gene and Identification of a Novel Lung-specific Binding Motif*. Journal Of Biological Chemistry 2003, 278: 15473-15483. PMID: 12598524, DOI: 10.1074/jbc.m300319200.Peer-Reviewed Original ResearchConceptsCYP2F1 geneCompetitive electrophoretic mobility shift assaysBacterial artificial chromosome (BAC) clonesElectrophoretic mobility shift assaysDNA-protein complexesE-box motifArtificial chromosome clonesPrimer extension analysisTranscription start siteTissue-specific expressionDNA consensus siteMobility shift assaysTissue-specific regulationUntranslated exon 1Transient transfection studiesLuciferase reporter constructsBox motifChromosome clonesConsensus sitesE-boxNuclear proteinsStart siteExtension analysisCDNA endsUpstream sequences
1995
Promoter elements conferring neuron-specific expression of the β2-subunit of the neuronal nicotinic acetylcholine receptor studiedin vitro and in transgenic mice
Bessis A, Salmon A, Zoli M, Le Novère N, Picciotto M, Changeux J. Promoter elements conferring neuron-specific expression of the β2-subunit of the neuronal nicotinic acetylcholine receptor studiedin vitro and in transgenic mice. Neuroscience 1995, 69: 807-819. PMID: 8596650, DOI: 10.1016/0306-4522(95)00303-z.Peer-Reviewed Original ResearchConceptsSpatio-temporal expression patternsFunctional E-boxesCell-specific transcriptionNeuron-specific transcriptionSite-directed mutagenesisTransient transfection assaysNeuron-specific expressionNeuronal genesRE1 sequenceTranscribed regionDeletion analysisE-boxRegulatory elementsPromoter elementsUpstream sequencesTransgenic miceTransfection assaysReporter geneRepressor elementExpression patternsNeuronal nicotinic acetylcholine receptorsGenesNicotinic acetylcholine receptorsRegulatory propertiesTranscription
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